PROJECT 3: Mapping the Evolution of Chronic Transplant Injury in the Context of CMV Infection SUMMARY/ABSTRACT CMV infection drives inflammation in the context of organ transplantation, and is associated with chronic rejection in the allograft, which drives accelerated allograft loss and transplant failure. The cascade of molecular mechanisms that trigger graft inflammation in the context of CMV infection are poorly understood. Whole genome, proteome, and immunome profiling of CMV infection and disease in the context of organ transplantation can generate a comprehensive global database to understand CMV infection and reactivation in an immunocompromised host and help design novel strategies to prevent viral reactivation and dampen anti- donor immunity. In Project 3, we propose to study the evolution of immune responses that drive acute rejection, chronic rejection, and CMV virus infection in kidney transplant recipients by serial assessments of graft transcriptional perturbations (Aim 1), clonal expansion of peripheral T cell and B cell receptors (TCRs and BCRs) through next gene expression sequencing (NGS), and variations in humoral responses to reactivation of antigenic epitopes by high-throughput antibody profiling (Aim 2). In addition, we propose to generate biomarkers for non-invasive monitoring of chronic graft injury by measuring changes in donor derived cell free DNA (dd-cfDNA) by massively multiplexed PCR (mmPCR) and highly refined gene-sets (kSORT and uCRM) mined from previous high-throughput microarray studies (Aim 3). We propose to use a cohort of kidney transplant patients from two of the largest multi-organ transplant programs in the US (UCSF and UCLA).